CLOCK.H12RSNP.1.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CLOCK.H12RSNP.1.PS.A
Gene (human)	CLOCK (GeneCards)
Gene synonyms (human)	BHLHE8, KIAA0334
Gene (mouse)	Clock
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	A

Motif length	14
Consensus	nnRCACGTGKChnn
GC content	58.17%
Information content (bits; total / per base)	14.809 / 1.058
Data sources	ChIP-Seq + HT-SELEX
Aligned words	7158

ChIP-Seq benchmarking	Num. of experiments (peaksets)	auROC, median	auROC, best	auPRC, median	auPRC, best	pseudo-auROC, median	pseudo-auROC, best	pseudo-log-auROC, median	pseudo-log-auROC, best	Centrality, median	Centrality, best
Human	3 (17)	0.761	0.804	0.693	0.724	0.734	0.798	2.299	2.594	51.076	133.469
Mouse	10 (66)	0.719	0.856	0.637	0.779	0.735	0.859	2.25	3.127	88.858	155.678

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.834	0.82	0.78	0.766	0.738	0.724
Overall, 4 experiments	best	0.998	0.996	0.997	0.995	0.995	0.992
Methyl HT-SELEX, 1 experiments	median	0.975	0.96	0.95	0.928	0.913	0.883
Methyl HT-SELEX, 1 experiments	best	0.975	0.96	0.95	0.928	0.913	0.883
Non-Methyl HT-SELEX, 3 experiments	median	0.692	0.68	0.61	0.605	0.564	0.566
Non-Methyl HT-SELEX, 3 experiments	best	0.998	0.996	0.997	0.995	0.995	0.992

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	1.45	0.381	0.115	0.062

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.95	0.872	0.93	0.565
batch 2	0.875	0.838	0.839	0.581

TF superclass	Basic domains {1} (TFClass)
TF class	Basic helix-loop-helix factors (bHLH) {1.2} (TFClass)
TF family	PAS {1.2.5} (TFClass)
TF subfamily	PAS-ARNT {1.2.5.2} (TFClass)
TFClass ID	TFClass: 1.2.5.2.5
HGNC	HGNC:2082
MGI	MGI:99698
EntrezGene (human)	GeneID:9575 (SSTAR profile)
EntrezGene (mouse)	GeneID:12753 (SSTAR profile)
UniProt ID (human)	CLOCK_HUMAN
UniProt ID (mouse)	CLOCK_MOUSE
UniProt AC (human)	O15516 (TFClass)
UniProt AC (mouse)	O08785 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	3 human, 10 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

PCM	CLOCK.H12RSNP.1.PS.A.pcm
PWM	CLOCK.H12RSNP.1.PS.A.pwm
PFM	CLOCK.H12RSNP.1.PS.A.pfm
Alignment	CLOCK.H12RSNP.1.PS.A.words.tsv
Threshold to P-value map	CLOCK.H12RSNP.1.PS.A.thr
Motif in other formats
JASPAR format	CLOCK.H12RSNP.1.PS.A_jaspar_format.txt
MEME format	CLOCK.H12RSNP.1.PS.A_meme_format.meme
Transfac format	CLOCK.H12RSNP.1.PS.A_transfac_format.txt
Homer format	CLOCK.H12RSNP.1.PS.A_homer_format_0.001.txt CLOCK.H12RSNP.1.PS.A_homer_format_0.0005.txt CLOCK.H12RSNP.1.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1952.75	1751.75	1780.75	1672.75
02	2453.0	1258.0	1576.0	1871.0
03	3977.0	1326.0	1835.0	20.0
04	0.0	7158.0	0.0	0.0
05	7158.0	0.0	0.0	0.0
06	0.0	7158.0	0.0	0.0
07	0.0	0.0	7158.0	0.0
08	0.0	0.0	0.0	7158.0
09	0.0	0.0	7158.0	0.0
10	0.0	633.0	3463.0	3062.0
11	60.0	6134.0	42.0	922.0
12	2452.0	2151.0	503.0	2052.0
13	1770.75	2040.75	1087.75	2258.75
14	1607.25	2079.25	2004.25	1467.25

PFM

	A	C	G	T
01	0.273	0.245	0.249	0.234
02	0.343	0.176	0.22	0.261
03	0.556	0.185	0.256	0.003
04	0.0	1.0	0.0	0.0
05	1.0	0.0	0.0	0.0
06	0.0	1.0	0.0	0.0
07	0.0	0.0	1.0	0.0
08	0.0	0.0	0.0	1.0
09	0.0	0.0	1.0	0.0
10	0.0	0.088	0.484	0.428
11	0.008	0.857	0.006	0.129
12	0.343	0.301	0.07	0.287
13	0.247	0.285	0.152	0.316
14	0.225	0.29	0.28	0.205

PWM

	A	C	G	T
01	0.087	-0.021	-0.005	-0.067
02	0.315	-0.352	-0.127	0.044
03	0.798	-0.299	0.025	-4.39
04	-6.694	1.385	-6.694	-6.694
05	1.385	-6.694	-6.694	-6.694
06	-6.694	1.385	-6.694	-6.694
07	-6.694	-6.694	1.385	-6.694
08	-6.694	-6.694	-6.694	1.385
09	-6.694	-6.694	1.385	-6.694
10	-6.694	-1.037	0.66	0.537
11	-3.36	1.231	-3.702	-0.662
12	0.315	0.184	-1.266	0.137
13	-0.011	0.131	-0.497	0.233
14	-0.107	0.15	0.113	-0.198

Standard thresholds

P-value	Threshold
0.001	-0.01421
0.0005	1.56377
0.0001	5.22821